Starting phenix.real_space_refine on Wed Sep 17 07:32:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iv2_60918/09_2025/9iv2_60918.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iv2_60918/09_2025/9iv2_60918.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iv2_60918/09_2025/9iv2_60918.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iv2_60918/09_2025/9iv2_60918.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iv2_60918/09_2025/9iv2_60918.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iv2_60918/09_2025/9iv2_60918.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4300 2.51 5 N 1134 2.21 5 O 1257 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6732 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2493 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 8, 'GLU:plan': 4, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 85 Chain: "G" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 417 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1756 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 5, 'GLN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "R" Number of atoms: 2045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2045 Classifications: {'peptide': 268} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 261} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'DHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.24 Number of scatterers: 6732 At special positions: 0 Unit cell: (76.36, 103.96, 124.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1257 8.00 N 1134 7.00 C 4300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 704 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 389.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 42.7% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 12 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.563A pdb=" N ALA G 23 " --> pdb=" O LEU G 19 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.568A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 38 removed outlier: 3.583A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 233 through 239 removed outlier: 4.119A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.561A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.159A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.672A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'R' and resid 566 through 591 Processing helix chain 'R' and resid 599 through 624 removed outlier: 3.736A pdb=" N HIS R 603 " --> pdb=" O ASN R 599 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG R 624 " --> pdb=" O LEU R 620 " (cutoff:3.500A) Processing helix chain 'R' and resid 629 through 662 removed outlier: 3.681A pdb=" N GLN R 633 " --> pdb=" O THR R 629 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL R 637 " --> pdb=" O GLN R 633 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU R 638 " --> pdb=" O VAL R 634 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 681 Processing helix chain 'R' and resid 681 through 694 removed outlier: 3.983A pdb=" N PHE R 693 " --> pdb=" O ILE R 689 " (cutoff:3.500A) Processing helix chain 'R' and resid 713 through 743 removed outlier: 3.797A pdb=" N ALA R 718 " --> pdb=" O TRP R 714 " (cutoff:3.500A) Proline residue: R 719 - end of helix Processing helix chain 'R' and resid 756 through 770 Proline residue: R 767 - end of helix Processing helix chain 'R' and resid 774 through 781 removed outlier: 3.932A pdb=" N LEU R 778 " --> pdb=" O VAL R 774 " (cutoff:3.500A) Processing helix chain 'R' and resid 788 through 797 removed outlier: 3.862A pdb=" N LEU R 797 " --> pdb=" O THR R 793 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 809 removed outlier: 3.756A pdb=" N PHE R 801 " --> pdb=" O LEU R 797 " (cutoff:3.500A) Processing helix chain 'R' and resid 810 through 827 removed outlier: 3.592A pdb=" N THR R 827 " --> pdb=" O VAL R 823 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.425A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 338 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.461A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.510A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN B 125 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.510A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.647A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG B 150 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU B 168 " --> pdb=" O THR B 178 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.597A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.372A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.989A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 286 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.662A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 219 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 214 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.851A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2185 1.34 - 1.46: 1150 1.46 - 1.58: 3483 1.58 - 1.70: 0 1.70 - 1.81: 56 Bond restraints: 6874 Sorted by residual: bond pdb=" C10 DHT R 901 " pdb=" C9 DHT R 901 " ideal model delta sigma weight residual 1.551 1.523 0.028 2.00e-02 2.50e+03 2.02e+00 bond pdb=" C13 DHT R 901 " pdb=" C14 DHT R 901 " ideal model delta sigma weight residual 1.534 1.511 0.023 2.00e-02 2.50e+03 1.33e+00 bond pdb=" C17 DHT R 901 " pdb=" O17 DHT R 901 " ideal model delta sigma weight residual 1.407 1.430 -0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" C10 DHT R 901 " pdb=" C5 DHT R 901 " ideal model delta sigma weight residual 1.546 1.524 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CB PRO R 767 " pdb=" CG PRO R 767 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.14e+00 ... (remaining 6869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 9277 2.19 - 4.39: 82 4.39 - 6.58: 13 6.58 - 8.78: 3 8.78 - 10.97: 2 Bond angle restraints: 9377 Sorted by residual: angle pdb=" CA LEU R 769 " pdb=" CB LEU R 769 " pdb=" CG LEU R 769 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.83e+00 angle pdb=" CB MET B 101 " pdb=" CG MET B 101 " pdb=" SD MET B 101 " ideal model delta sigma weight residual 112.70 121.13 -8.43 3.00e+00 1.11e-01 7.90e+00 angle pdb=" C TRP R 649 " pdb=" N MET R 650 " pdb=" CA MET R 650 " ideal model delta sigma weight residual 120.31 116.28 4.03 1.52e+00 4.33e-01 7.03e+00 angle pdb=" CA LEU G 15 " pdb=" CB LEU G 15 " pdb=" CG LEU G 15 " ideal model delta sigma weight residual 116.30 125.56 -9.26 3.50e+00 8.16e-02 7.00e+00 angle pdb=" N ILE R 713 " pdb=" CA ILE R 713 " pdb=" C ILE R 713 " ideal model delta sigma weight residual 112.98 109.72 3.26 1.25e+00 6.40e-01 6.82e+00 ... (remaining 9372 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3466 18.00 - 35.99: 449 35.99 - 53.99: 125 53.99 - 71.98: 11 71.98 - 89.98: 11 Dihedral angle restraints: 4062 sinusoidal: 1466 harmonic: 2596 Sorted by residual: dihedral pdb=" CB CYS R 632 " pdb=" SG CYS R 632 " pdb=" SG CYS R 704 " pdb=" CB CYS R 704 " ideal model delta sinusoidal sigma weight residual 93.00 144.51 -51.51 1 1.00e+01 1.00e-02 3.62e+01 dihedral pdb=" CB GLU B 3 " pdb=" CG GLU B 3 " pdb=" CD GLU B 3 " pdb=" OE1 GLU B 3 " ideal model delta sinusoidal sigma weight residual 0.00 -89.98 89.98 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU R 653 " pdb=" CG GLU R 653 " pdb=" CD GLU R 653 " pdb=" OE1 GLU R 653 " ideal model delta sinusoidal sigma weight residual 0.00 -84.77 84.77 1 3.00e+01 1.11e-03 9.69e+00 ... (remaining 4059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 935 0.054 - 0.108: 155 0.108 - 0.163: 16 0.163 - 0.217: 2 0.217 - 0.271: 1 Chirality restraints: 1109 Sorted by residual: chirality pdb=" C10 DHT R 901 " pdb=" C1 DHT R 901 " pdb=" C5 DHT R 901 " pdb=" C9 DHT R 901 " both_signs ideal model delta sigma weight residual False -2.97 -2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C13 DHT R 901 " pdb=" C12 DHT R 901 " pdb=" C14 DHT R 901 " pdb=" C17 DHT R 901 " both_signs ideal model delta sigma weight residual False -2.87 -2.67 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA PRO R 767 " pdb=" N PRO R 767 " pdb=" C PRO R 767 " pdb=" CB PRO R 767 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.17 2.00e-01 2.50e+01 7.53e-01 ... (remaining 1106 not shown) Planarity restraints: 1188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 360 " -0.059 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO A 361 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 DHT R 901 " 0.017 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C3 DHT R 901 " -0.055 2.00e-02 2.50e+03 pdb=" C4 DHT R 901 " 0.017 2.00e-02 2.50e+03 pdb=" O3 DHT R 901 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU R 766 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO R 767 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO R 767 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 767 " -0.041 5.00e-02 4.00e+02 ... (remaining 1185 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 391 2.73 - 3.27: 6889 3.27 - 3.81: 10887 3.81 - 4.36: 11181 4.36 - 4.90: 20012 Nonbonded interactions: 49360 Sorted by model distance: nonbonded pdb=" O LEU R 566 " pdb=" OG SER R 570 " model vdw 2.186 3.040 nonbonded pdb=" OG1 THR B 165 " pdb=" O PHE B 180 " model vdw 2.263 3.040 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.269 3.040 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.307 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.307 3.040 ... (remaining 49355 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.400 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 6875 Z= 0.105 Angle : 0.539 10.974 9379 Z= 0.268 Chirality : 0.040 0.271 1109 Planarity : 0.004 0.089 1188 Dihedral : 17.472 89.977 2375 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 37.75 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.29), residues: 880 helix: 1.74 (0.29), residues: 354 sheet: 0.81 (0.53), residues: 118 loop : -2.16 (0.28), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.005 0.001 TYR A 263 PHE 0.012 0.001 PHE A 340 TRP 0.009 0.001 TRP A 277 HIS 0.002 0.000 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 6874) covalent geometry : angle 0.53887 ( 9377) SS BOND : bond 0.00411 ( 1) SS BOND : angle 0.61197 ( 2) hydrogen bonds : bond 0.15353 ( 303) hydrogen bonds : angle 6.17547 ( 903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.257 Fit side-chains REVERT: A 34 LYS cc_start: 0.9241 (tppp) cc_final: 0.8965 (tppt) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.0831 time to fit residues: 10.6488 Evaluate side-chains 85 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.079932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.066852 restraints weight = 19948.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.068317 restraints weight = 8156.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.069198 restraints weight = 4577.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.069723 restraints weight = 3147.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.070049 restraints weight = 2515.452| |-----------------------------------------------------------------------------| r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6875 Z= 0.133 Angle : 0.502 7.464 9379 Z= 0.264 Chirality : 0.039 0.143 1109 Planarity : 0.004 0.064 1188 Dihedral : 3.717 35.641 1000 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 5.19 % Allowed : 32.56 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.29), residues: 880 helix: 1.65 (0.29), residues: 365 sheet: 0.51 (0.48), residues: 136 loop : -2.28 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.008 0.001 TYR R 602 PHE 0.014 0.001 PHE A 340 TRP 0.009 0.001 TRP B 99 HIS 0.002 0.001 HIS R 672 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6874) covalent geometry : angle 0.50228 ( 9377) SS BOND : bond 0.00557 ( 1) SS BOND : angle 0.48022 ( 2) hydrogen bonds : bond 0.03907 ( 303) hydrogen bonds : angle 4.98302 ( 903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.241 Fit side-chains REVERT: B 13 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6652 (pm20) REVERT: B 285 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8597 (tp) REVERT: A 34 LYS cc_start: 0.9164 (tppp) cc_final: 0.8939 (tppt) outliers start: 36 outliers final: 20 residues processed: 114 average time/residue: 0.0723 time to fit residues: 11.3204 Evaluate side-chains 102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 601 ARG Chi-restraints excluded: chain R residue 644 LEU Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 768 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 44 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.077172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.064072 restraints weight = 19846.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.065461 restraints weight = 8197.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.066342 restraints weight = 4666.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.066889 restraints weight = 3229.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.067145 restraints weight = 2575.967| |-----------------------------------------------------------------------------| r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6875 Z= 0.195 Angle : 0.528 5.573 9379 Z= 0.280 Chirality : 0.040 0.140 1109 Planarity : 0.004 0.054 1188 Dihedral : 3.980 40.538 1000 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 5.04 % Allowed : 31.27 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.29), residues: 880 helix: 1.38 (0.28), residues: 366 sheet: 0.47 (0.47), residues: 141 loop : -2.34 (0.28), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.011 0.001 TYR R 602 PHE 0.016 0.001 PHE A 340 TRP 0.008 0.001 TRP R 680 HIS 0.003 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 6874) covalent geometry : angle 0.52818 ( 9377) SS BOND : bond 0.00889 ( 1) SS BOND : angle 0.58261 ( 2) hydrogen bonds : bond 0.04122 ( 303) hydrogen bonds : angle 5.02839 ( 903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 76 time to evaluate : 0.255 Fit side-chains REVERT: B 13 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6544 (pm20) REVERT: R 579 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7405 (tt) outliers start: 35 outliers final: 23 residues processed: 100 average time/residue: 0.0695 time to fit residues: 9.7889 Evaluate side-chains 96 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 802 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.079222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.066060 restraints weight = 19977.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.067510 restraints weight = 8151.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.068399 restraints weight = 4587.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.068932 restraints weight = 3166.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.069343 restraints weight = 2533.755| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6875 Z= 0.121 Angle : 0.499 7.974 9379 Z= 0.259 Chirality : 0.039 0.159 1109 Planarity : 0.003 0.046 1188 Dihedral : 3.838 40.231 1000 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.18 % Allowed : 32.56 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.29), residues: 880 helix: 1.58 (0.28), residues: 364 sheet: 0.38 (0.47), residues: 136 loop : -2.30 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 256 TYR 0.008 0.001 TYR R 602 PHE 0.013 0.001 PHE A 340 TRP 0.008 0.001 TRP A 277 HIS 0.002 0.001 HIS R 640 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6874) covalent geometry : angle 0.49943 ( 9377) SS BOND : bond 0.00437 ( 1) SS BOND : angle 0.38159 ( 2) hydrogen bonds : bond 0.03613 ( 303) hydrogen bonds : angle 4.76284 ( 903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.259 Fit side-chains REVERT: B 13 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.6588 (pm20) REVERT: B 285 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8616 (tp) REVERT: A 34 LYS cc_start: 0.9149 (tppp) cc_final: 0.8908 (tppt) REVERT: R 579 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7419 (tt) REVERT: R 669 ASP cc_start: 0.9449 (OUTLIER) cc_final: 0.8842 (t0) REVERT: R 814 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7070 (mtm-85) outliers start: 29 outliers final: 18 residues processed: 99 average time/residue: 0.0677 time to fit residues: 9.4407 Evaluate side-chains 94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 31 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 54 optimal weight: 0.0040 chunk 37 optimal weight: 0.0170 chunk 9 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.8834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.081123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.067907 restraints weight = 19801.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.069393 restraints weight = 8000.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.070312 restraints weight = 4487.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.070906 restraints weight = 3078.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.071119 restraints weight = 2418.783| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6875 Z= 0.100 Angle : 0.480 7.784 9379 Z= 0.250 Chirality : 0.038 0.134 1109 Planarity : 0.003 0.041 1188 Dihedral : 3.697 40.239 1000 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.61 % Allowed : 33.00 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.29), residues: 880 helix: 1.79 (0.29), residues: 358 sheet: 0.24 (0.48), residues: 134 loop : -2.27 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.007 0.001 TYR R 658 PHE 0.012 0.001 PHE A 340 TRP 0.008 0.001 TRP A 277 HIS 0.001 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 6874) covalent geometry : angle 0.47959 ( 9377) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.35003 ( 2) hydrogen bonds : bond 0.03348 ( 303) hydrogen bonds : angle 4.54771 ( 903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 0.257 Fit side-chains REVERT: B 13 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6731 (pm20) REVERT: B 285 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8660 (tp) REVERT: A 34 LYS cc_start: 0.9116 (tppp) cc_final: 0.8897 (tppt) REVERT: A 389 ARG cc_start: 0.9160 (tpm170) cc_final: 0.8843 (tpm170) REVERT: R 579 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7368 (tt) REVERT: R 625 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8226 (tt) REVERT: R 669 ASP cc_start: 0.9436 (OUTLIER) cc_final: 0.8901 (t0) outliers start: 32 outliers final: 17 residues processed: 108 average time/residue: 0.0695 time to fit residues: 10.4719 Evaluate side-chains 101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 768 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 36 optimal weight: 7.9990 chunk 29 optimal weight: 0.0980 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.0570 chunk 47 optimal weight: 4.9990 chunk 9 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.8304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.078825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.065597 restraints weight = 20153.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.067025 restraints weight = 8218.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.067908 restraints weight = 4635.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.068431 restraints weight = 3194.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.068820 restraints weight = 2560.541| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6875 Z= 0.143 Angle : 0.510 8.438 9379 Z= 0.265 Chirality : 0.039 0.138 1109 Planarity : 0.003 0.039 1188 Dihedral : 3.791 39.380 1000 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.04 % Allowed : 32.42 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.29), residues: 880 helix: 1.58 (0.28), residues: 365 sheet: 0.22 (0.46), residues: 139 loop : -2.30 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.008 0.001 TYR R 789 PHE 0.015 0.001 PHE A 340 TRP 0.007 0.001 TRP B 99 HIS 0.002 0.001 HIS R 605 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6874) covalent geometry : angle 0.51038 ( 9377) SS BOND : bond 0.00597 ( 1) SS BOND : angle 0.44983 ( 2) hydrogen bonds : bond 0.03651 ( 303) hydrogen bonds : angle 4.65812 ( 903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 0.257 Fit side-chains REVERT: B 13 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6631 (pm20) REVERT: B 285 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8622 (tp) REVERT: A 34 LYS cc_start: 0.9140 (tppp) cc_final: 0.8900 (tppt) REVERT: A 211 LYS cc_start: 0.8858 (mmmm) cc_final: 0.8649 (mmmm) REVERT: R 579 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7416 (tt) REVERT: R 625 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8382 (tt) REVERT: R 669 ASP cc_start: 0.9448 (OUTLIER) cc_final: 0.8845 (t0) REVERT: R 814 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7080 (mtm-85) outliers start: 35 outliers final: 27 residues processed: 102 average time/residue: 0.0722 time to fit residues: 10.2568 Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 84 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 79 optimal weight: 0.0070 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.082386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.069261 restraints weight = 19436.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.070704 restraints weight = 8037.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.071611 restraints weight = 4550.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.072176 restraints weight = 3142.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.072512 restraints weight = 2492.852| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6875 Z= 0.096 Angle : 0.485 8.326 9379 Z= 0.249 Chirality : 0.038 0.133 1109 Planarity : 0.003 0.038 1188 Dihedral : 3.621 38.473 1000 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.47 % Allowed : 33.29 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.29), residues: 880 helix: 1.86 (0.29), residues: 358 sheet: 0.16 (0.47), residues: 134 loop : -2.21 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.007 0.001 TYR R 658 PHE 0.011 0.001 PHE A 340 TRP 0.008 0.001 TRP R 649 HIS 0.001 0.000 HIS R 806 Details of bonding type rmsd covalent geometry : bond 0.00202 ( 6874) covalent geometry : angle 0.48519 ( 9377) SS BOND : bond 0.00270 ( 1) SS BOND : angle 0.31411 ( 2) hydrogen bonds : bond 0.03257 ( 303) hydrogen bonds : angle 4.41396 ( 903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 83 time to evaluate : 0.293 Fit side-chains REVERT: B 13 GLN cc_start: 0.7384 (OUTLIER) cc_final: 0.6689 (pm20) REVERT: B 225 HIS cc_start: 0.8481 (OUTLIER) cc_final: 0.8130 (t-170) REVERT: B 285 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8632 (tp) REVERT: A 34 LYS cc_start: 0.9102 (tppp) cc_final: 0.8872 (tppt) REVERT: A 389 ARG cc_start: 0.9162 (tpm170) cc_final: 0.8585 (tpm170) REVERT: R 579 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7385 (tt) REVERT: R 669 ASP cc_start: 0.9424 (OUTLIER) cc_final: 0.8934 (t0) REVERT: R 814 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7142 (mtm-85) outliers start: 31 outliers final: 17 residues processed: 106 average time/residue: 0.0764 time to fit residues: 11.0959 Evaluate side-chains 100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 70 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 68 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.081956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.068754 restraints weight = 19788.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.070247 restraints weight = 7987.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.071167 restraints weight = 4448.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.071757 restraints weight = 3042.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.072139 restraints weight = 2388.978| |-----------------------------------------------------------------------------| r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6875 Z= 0.102 Angle : 0.492 7.475 9379 Z= 0.255 Chirality : 0.038 0.137 1109 Planarity : 0.003 0.036 1188 Dihedral : 3.558 36.117 1000 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.61 % Allowed : 33.14 % Favored : 62.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.29), residues: 880 helix: 1.79 (0.28), residues: 364 sheet: 0.20 (0.47), residues: 134 loop : -2.22 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.007 0.001 TYR A 263 PHE 0.012 0.001 PHE A 340 TRP 0.007 0.001 TRP R 649 HIS 0.001 0.000 HIS R 806 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 6874) covalent geometry : angle 0.49239 ( 9377) SS BOND : bond 0.00338 ( 1) SS BOND : angle 0.28387 ( 2) hydrogen bonds : bond 0.03252 ( 303) hydrogen bonds : angle 4.38009 ( 903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 82 time to evaluate : 0.256 Fit side-chains REVERT: B 13 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6742 (pm20) REVERT: B 225 HIS cc_start: 0.8450 (OUTLIER) cc_final: 0.8086 (t-170) REVERT: B 285 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8608 (tp) REVERT: A 34 LYS cc_start: 0.9094 (tppp) cc_final: 0.8862 (tppt) REVERT: A 389 ARG cc_start: 0.9140 (tpm170) cc_final: 0.8541 (tpm170) REVERT: R 579 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7340 (tt) REVERT: R 625 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8193 (tt) REVERT: R 669 ASP cc_start: 0.9429 (OUTLIER) cc_final: 0.8975 (t0) REVERT: R 814 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7170 (mtm-85) outliers start: 32 outliers final: 21 residues processed: 107 average time/residue: 0.0741 time to fit residues: 10.8025 Evaluate side-chains 106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 37 optimal weight: 0.0070 chunk 17 optimal weight: 5.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.077285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.064091 restraints weight = 20290.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.065478 restraints weight = 8312.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.066326 restraints weight = 4734.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.066825 restraints weight = 3284.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.067226 restraints weight = 2636.769| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6875 Z= 0.215 Angle : 0.566 7.965 9379 Z= 0.296 Chirality : 0.041 0.167 1109 Planarity : 0.003 0.036 1188 Dihedral : 4.013 41.153 1000 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 5.04 % Allowed : 32.85 % Favored : 62.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.29), residues: 880 helix: 1.39 (0.28), residues: 365 sheet: 0.27 (0.47), residues: 138 loop : -2.26 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.011 0.001 TYR A 318 PHE 0.018 0.001 PHE A 340 TRP 0.014 0.001 TRP B 99 HIS 0.003 0.001 HIS R 672 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 6874) covalent geometry : angle 0.56633 ( 9377) SS BOND : bond 0.00959 ( 1) SS BOND : angle 0.49877 ( 2) hydrogen bonds : bond 0.04085 ( 303) hydrogen bonds : angle 4.87982 ( 903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.249 Fit side-chains REVERT: B 13 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: B 285 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8766 (tp) REVERT: A 34 LYS cc_start: 0.9168 (tppp) cc_final: 0.8923 (tppt) REVERT: R 579 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7389 (tt) REVERT: R 625 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8484 (tt) REVERT: R 669 ASP cc_start: 0.9476 (OUTLIER) cc_final: 0.8882 (t0) REVERT: R 814 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7080 (mtm-85) outliers start: 35 outliers final: 25 residues processed: 99 average time/residue: 0.0741 time to fit residues: 10.2698 Evaluate side-chains 100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 645 SER Chi-restraints excluded: chain R residue 652 VAL Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 768 ILE Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 58 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.080675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.067436 restraints weight = 19737.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.068896 restraints weight = 7996.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.069786 restraints weight = 4503.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.070329 restraints weight = 3094.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.070568 restraints weight = 2468.850| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6875 Z= 0.107 Angle : 0.526 9.367 9379 Z= 0.268 Chirality : 0.039 0.152 1109 Planarity : 0.003 0.035 1188 Dihedral : 3.771 41.205 1000 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.75 % Allowed : 34.29 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.29), residues: 880 helix: 1.73 (0.28), residues: 358 sheet: 0.19 (0.46), residues: 137 loop : -2.21 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.007 0.001 TYR R 658 PHE 0.012 0.001 PHE A 340 TRP 0.011 0.001 TRP R 649 HIS 0.001 0.000 HIS R 605 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6874) covalent geometry : angle 0.52607 ( 9377) SS BOND : bond 0.00460 ( 1) SS BOND : angle 0.35446 ( 2) hydrogen bonds : bond 0.03399 ( 303) hydrogen bonds : angle 4.52120 ( 903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.235 Fit side-chains REVERT: B 13 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6626 (pm20) REVERT: B 217 MET cc_start: 0.7360 (tmm) cc_final: 0.7056 (tmm) REVERT: B 285 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8671 (tp) REVERT: A 34 LYS cc_start: 0.9116 (tppp) cc_final: 0.8887 (tppt) REVERT: A 389 ARG cc_start: 0.9178 (tpm170) cc_final: 0.8807 (tpm170) REVERT: R 579 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7358 (tt) REVERT: R 625 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8307 (tt) REVERT: R 669 ASP cc_start: 0.9444 (OUTLIER) cc_final: 0.8817 (t0) REVERT: R 814 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7100 (mtm-85) outliers start: 26 outliers final: 19 residues processed: 97 average time/residue: 0.0741 time to fit residues: 9.9121 Evaluate side-chains 101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 290 PHE Chi-restraints excluded: chain R residue 564 VAL Chi-restraints excluded: chain R residue 579 LEU Chi-restraints excluded: chain R residue 582 VAL Chi-restraints excluded: chain R residue 625 LEU Chi-restraints excluded: chain R residue 669 ASP Chi-restraints excluded: chain R residue 726 VAL Chi-restraints excluded: chain R residue 814 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 19 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.079127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.065918 restraints weight = 19871.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.067337 restraints weight = 8113.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.068236 restraints weight = 4594.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.068794 restraints weight = 3161.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.069123 restraints weight = 2508.152| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6875 Z= 0.143 Angle : 0.544 10.665 9379 Z= 0.277 Chirality : 0.040 0.177 1109 Planarity : 0.003 0.036 1188 Dihedral : 3.797 39.048 1000 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.18 % Allowed : 34.01 % Favored : 61.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.29), residues: 880 helix: 1.53 (0.28), residues: 365 sheet: 0.18 (0.48), residues: 132 loop : -2.23 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.007 0.001 TYR R 789 PHE 0.015 0.001 PHE A 340 TRP 0.010 0.001 TRP B 99 HIS 0.002 0.001 HIS R 672 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6874) covalent geometry : angle 0.54387 ( 9377) SS BOND : bond 0.00580 ( 1) SS BOND : angle 0.44822 ( 2) hydrogen bonds : bond 0.03634 ( 303) hydrogen bonds : angle 4.63446 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.01 seconds wall clock time: 21 minutes 30.45 seconds (1290.45 seconds total)